plotMA {codelink}R Documentation

MA plot

Description

Takes a Codelink object and plot M vs A.

Usage

  plotMA(object, array1=1, array2=2, cutoff=NULL, label="type", type=NULL,
        high.list=NULL, high.col="blue", high.pch="*",
        snr.cutoff=1, legend.x="bottomright", pch=".", subset=NULL, 
        title=NULL, xlim=NULL, ylim=NULL)

Arguments

object an object of class "Codelink" or "MAarrayLM".
array1 first array to be used.
array2 second array to be used.
cutoff cutoff to be used as fold change markeer.
label type of labeling used in legend.
type spot type information.
high.list list of genes highlighted.
high.col color used for high genes.
high.pch pch used for high genes.
snr.cutoff SNR cutoff used for label spots.
legend.x relative position of the legend.
pch pch style used to main spots.
subset subset of spots used to plot based on 'type' slot.
title title of the plot.
xlim range for the X axis.
ylim range for the Y axis.

Details

The plot is for M=(array2-array1) vs A=(array2+array1)/2.

Value

Note

Author(s)

Diego Diez

See Also

Examples

#    data(codelink.example)
#    plotMA(codelink.example)

[Package codelink version 1.4.0 Index]